AMBER Archive (2002)

Subject: Order of a protein, bound waters and ligand in saveamberparm

From: Masaki Tomimoto (masaki_at_stromix.com)
Date: Thu Aug 15 2002 - 15:25:45 CDT

Hi All

   I have a question about a command "saveamberparm" in "tleap".

   I have a pdb file which contains a protein, bound waters and a ligand in this order. In order to differentiate the bound waters from solvent waters, I named the bound waters as "CTW" instead of "WAT, HOH, TP3" and created a library file "CTW.lib" which contains the same information as "TP3" in "solvent.lib". In the pdb file, residue number and atom number are assigned sequentially. In "tleap", I executed the following commands

   source leaprc.ff99
   loadoff CTW.lib
   loadamberprep ligand.prep
   loadamperparams frcmod
   pdb = loadpdb target.pdb
   saveamberparm pdb target.top target.x

   Whereas the original pdb file contains a protein, bound waters, and a ligand, its output contains the protein, the ligand, and bound waters in this order. It seems to me that "saveamberparm" command kindly sorted them even if I gave a special residue name to bound waters. I would like to keep the order of protein, bound waters and ligand. Is there anyway to avoid the sorting? Did I make any mistake?

Thank you in advance

Masaki Tomimoto